AGAROSE RESOLVABLE INDEL MARKERS BASED ON WHOLE GENOME RE SEQUENCING IN CUCUMBER
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OPEN Agarose‑resolvable InDel
markers based on whole genome
re‑sequencing in cucumber
Yawo Mawunyo Nevame Adedze1*, Xia Lu1, Yingchun Xia1, Qiuyue Sun1,
Chofong G. Nchongboh2, Md. Amirul Alam3, Menghua Liu1, Xue Yang1, Wenting Zhang1,
Zhijun Deng1, Wenhu Li1 & Longting Si1
Insertion and Deletion (InDel) are common features in genomes and are associated with genetic
variation. The whole-genome re-sequencing data from two parents (X1 and X2) of the elite cucumber
(Cucumis sativus) hybrid variety Lvmei No.1 was used for genome-wide InDel polymorphisms analysis.
Obtained sequence reads were mapped to the genome reference sequence of Chinese fresh market
type inbred line ‘9930’ and gaps conforming to InDel were pinpointed. Further, the level of cross-
parents polymorphism among five pairs of cucumber breeding parents and their corresponding hybrid
varieties were used for evaluating hybrid seeds purity test efficiency of InDel markers. A panel of 48
cucumber breeding lines was utilized for PCR amplification versatility and phylogenetic analysis of
these markers. In total, 10,470 candidate InDel markers were identified for X1 and X2. Among these,
385 markers with more than 30 nucleotide difference were arbitrary chosen. These markers were
selected for experimental resolvability through electrophoresis on an Agarose gel. Two hundred and
eleven (211) accounting for 54.81% of markers could be validated as single and clear polymorphic
pattern while 174 (45.19%) showed unclear or monomorphic genetic bands between X1 and X2. Cross-
parents polymorphism evaluation recorded 68 (32.23%) of these markers, which were designated
as cross-parents transferable (CPT) InDel markers. Interestingly, the marker InDel114 presented
experimental transferability between cucumber and melon. A panel of 48 cucumber breeding lines
including parents of Lvmei No. 1 subjected to PCR amplification versatility using CPT InDel markers
successfully clustered them into fruit and common cucumber varieties based on phylogenetic analysis.
It is worth noting that 16 of these markers were predominately associated to enzymatic activities in
cucumber. These agarose-based InDel markers could constitute a valuable resource for hybrid seeds
purity testing, germplasm classification and marker-assisted breeding in cucumber.
Cucumber (Cucumis sativus) is one of the many important creeping vine vegetables. It belongs to the fam-
ily Cucurbitaceae in the plant kingdom comprising several economically important species including melons,
watermelon, squashes, and pumpkins. The Asia continent is being examined as a center for the first domestica-
tion as far back as 1500 BC1,2. Cucumber has relatively encountered genetic bottleneck all through the era of
domestication, thus restricting its genetic background. In allusion to melon, following natural and artificial
selection, the genetic variation of cultivated cucumber varieties are greatly reduced3–5. In consequence, it is easy
to compromise morphological identification of cucumber genotypes due to environmental factors, especially
with closely related genotypes. There has been credible advancement in the development of assorted types of
DNA markers for a better phenotypic discrimination of cucumber varieties.
Restriction fragment length polymorphisms (RFLP) and amplified fragment length polymorphisms (AFLP)
are the earliest types of DNA markers identified through DNA digestion with restriction enzymes, followed by
hybridization with isotope-labeled or biotin-labeled p robes6–8. The disadvantages of these markers were attrib-
uted to their time-consuming nature for detection and detrimental environmental effects as narrated by Hu and
colleagues9. Random amplified polymorphic DNAs (RAPD)10,11 and simple sequences repeats (SSR)12,13 are mark-
ers developed on the basis of Polymerase Chain Reaction (PCR) resolvable by polyacrylamide gel electrophoresis.
1
Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company,
Suqian 223800, Jiangsu, China. 2Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants,
Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11‑12, 38104 Brunswick, Germany. 3Faculty of
Sustainable Agriculture, Horticulture and Landscaping Program, University Malaysia Sabah, Sandakan Campus,
90509 Sandakan, Sabah, Malaysia. *email: amen.nevame07@yahoo.fr
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With reference to cucumber, these two generation of markers have proven a relatively low intraspecific genetic
diversity (3–12%) in contrast to other member species of the genus Cucumis, consequently influencing their
application in high-resolution m apping14–18.
The genomic sequence accessibility of Chinese fresh market type inbred line ‘9930’, the North American pick-
ling type inbred line ‘Gy14’ together with the high-quality genome assembly of North European cucumber have
served as a furnishing tool in accelerating and facilitating the genome-wide, large-scale development of molecular
markers in cucumber19–21. Henceforth, a number of cross-species transferable SSR markers have been developed
based on draft genome assemblies between cucumber, melon and watermelon22–27. Be that as it may, the robust-
ness, informative and user-friendly SSR markers publicly available (10–20%) in intraspecific polymorphism
application in cucumber is still limited28,29. In addition, accessibility to electrophoresis equipment’s might not be
easy for most breeders as it is required for polyacrylamide gel separation in course of developing SSR markers.
Owning to the recent progress in re-sequencing technology, the third generation of DNA markers is based
on single nucleotide polymorphism (SNP) and insertion/deletion (InDel) for the production of SNP and InDel
markers, respectively30. These two categories of markers (SNPs and InDel) are known for their co-dominancy
and genome-wide distribution and are importantly exploited in plant genetic studies. Discovery and construction
of SNP-based saturated linkage map have been reported in cucumber, which has facilitated the genetic mapping
of complex QTL loci controlling cucumber agronomic traits31,32. Nonetheless, a genotyping with SNP marker is
based on sequencing and/or on SNP arrays, which are rarely performed in most breeding units. SNP genotyp-
ing is thereby mostly performed by commercial companies, and this is known to be a time-consuming process
for the generation and achievement of a reasonable data. Early this year, Zhang and his team reported a new
SNP genotyping in cucumber based on multiplex PCR amplification and high throughput s equencing33. InDel
molecular markers provide advantages in different fold including high accuracy and high stability which help in
deciphering the confusion that may arise in genetic analysis as compared to other length polymorphic markers.
Moreover, they can amplify target fragments from mixed or highly degraded DNA samples34. InDel markers have
been developed for several crops including cotton, rice, maize, rapeseed, cucumber etc35–41. It is clear that some
polymorphic InDel markers were previously developed for genotyping of cucumber and has been applied on 6
typical cucumber g ermplasm42 nonetheless; they were all resolvable on polyacrylamide gel due to the InDel sizes.
Based on our knowledge and technical know-how, the use of agarose gel electrophoresis in genotyping is
easily accepted by breeders due to its simple requirements and easy operation in the laboratory compared to
polyacrylamide electrophoresis. We therefore, deemed it significant that developing Agarose resovable InDel
markers will be a mile stone in marker development for breeders in breeding programs. This will ease and
increase efficiency of plants genotyping by accelerating the procedure during breeding programs. Although,
InDel markers can be developed for both polyacrylamide and agarose gel electrophoresis depending on their
sizes36. High-density Insertion/Deletion is needed which could be exploited for the discovery of valuable InDel
markers for genotypes screening through agarose gel rather than polyacrylamide g el40. Thus, availability of a
large number of genome-wide InDel makers is essential to reach this goal.
In this study, we developed agarose-resolvable InDel markers through re-sequencing whole genomes and
identify genetic variation (insertion and deletion) for the breeding parents X1 and X2 of cucumber hybrid variety
Lvmei No.1 compared to the reference genome sequence of Chinese fresh market type inbred line ‘9930’. The
development and detection of these InDel markers relied greatly on the separation of their PCR products by
agarose gel electrophoresis, investigation on their polymorphism and crossed-parents transferability. The later
was conducted using varied number of breeding parent including five (5) pairs for cucumber, three (3) pairs of
melon and two (2) pairs of watermelon. A total of forty-eight (48) cucumber breeding lines were evaluated for
PCR amplification versatility and phylogenetic analysis using the developed InDel markers. These InDel markers
are regarded as useful genetic reservoir for genotypes identification, genetic diversity analysis, hybrid testing and
marker assisted selection in cucumber breeding programs.
Materials and methods
Plant materials. Two cucumber lines designated as X1 and X2 constituting the parents of an elite com-
mercial hybrid Lvmei No. 1 were used for whole genome re-sequencing (Supplemental Table S1A). These breed-
ing parents are derivative of three different commercial varieties 22–403, Zhongnong No. 26 and HA-414. The
hybrid varieties 22–403 and Zhongnong No. 26 developed by RijkZwaan Company and Institute of Vegetables
and Flowers of the Chinese Academy of Agricultural Sciences (CAAS, respectively. Hybrid variety 22–403 is
prominent for its good taste, cold tolerance trait, and year-round greenhouse cultivation while strong growth
potential, comprehensive diseases resistance and tolerance to low temperature and light intensity characterize
Zhongnong No. 26. The third is the fruit cucumber variety HA-414 which was imported from Israel. Crossing
between 22 and 403 and Zhongnong No. 26 accompanied by seven generations of selfing gave rise to the male
parent of Lvmei No. 1 (X2). This variety (X2) is prominent for its late-maturity in addition to its outstanding
growth character, sweet fruit and high resistance to downy mildew. The female parent (X1) was obtained after
six generations of selfing of HA-414. X1 is distinguished for its early maturity, with relative resistance to downy
mildew incorporated with sweet and good fruit set. Moreover, pairs of cucumber C1/C2, C3/C4, C5/C6, C7/
C8; melon M1/M2, M3/M4, M5/M6; watermelon W1/W2 and W1/W2 commercial hybrids were utilized for
cross-parents polymorphism analysis (Suppl. Table S1B). Forty-eight cucumber breeding lines, classified into
three groups (1, 2 and 3) grounded on their fruit morphology, were used for InDel markers versatility and
phylogenetic analysis. Group 1 and 2 composed of 23 dense spiny cucumber lines and 18 fruit cucumber lines,
respectively. Group 3 constituted 6 white-green sparsely spiny and 2 yellow-green sparsely spiny cucumber lines
(Suppl. Table S1). The representative fruit morphology for each group of cucumber lines including X1 and X2,
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and hybrid variety LvmeiNo.1 are detailed in Fig. 1A–I. All the plants were grown in solar greenhouse of Jiangsu
Green Port Modern Agriculture Development Company.
Library construction and sequencing. CTAB extraction method was used to isolate genomic DNA
from fresh leaves of 30 days old X1 and X2 plants maintained in the greenhouse. The quality of extracted DNA
was evaluated by electrophoresis, running an aliquot of 5 µl on a 1% agarose gel and concentration measured
with Nanodrop spectrophotometer 2000 (Thermo Scientific, USA). Samples whose genomic DNA measured
more > 10 ng/µL at an OD260/280 with values between 1.8 and 2.0 were considered for library construction.
Initially, genomic DNA was sheared using an ultrasonic Crusher (Ultrasonic Crusher Q800R3, Qsonica Co
Ltd, USA) to yield an average DNA fragments of about 350 base pair (bp). These fragmented DNA samples
were cleaned up using AMPure XP beads (http://www.beckmancoulter.cn) and freshly prepared 80% Ethanol
according to manufacturer’s protocol. Subsequently, DNA ends repair, library size selection, adenylation, Illu-
mina paired-end adapter’s ligation to fragmented DNA were performed successively. The ligated DNA products
were selected and amplified. Two paired-end libraries with 15-fold depth for each cucumber breeding line was
constructed using TruSeq DNA LT Sample Prep kit. The resulting libraries were sequenced on an Illumina Hiseq
X Ten, PE150sequencer (Shanghai OE Biotech. Co. Ltd, China).In this work, all steps were conducted according
to OE Biotech Company deep sequencing protocol (Shanghai OE Biotech. Co. Ltd, China).
Data filtering, alignment and variants calling. Cucumis sativus L. var. sativus cv. Chinese fresh market
type inbred line ‘9930’ genome sequence was obtained from cucurbit genomics database (CuGenDB) (ftp://
cucurbitgenomics.org/pub/cucurbit/genome/cucumber/Chinese_long) and was used as the reference sequence.
Low quality reads data were filtered out using a custom C program based on the default parameters to recover
clean reads data. The cleaned reads data were aligned to the reference genome with the help of BWA (BWA0.7.10-
r789) program43. The alignment output results in SAM format were then converted into Binary Alignment Map
(BAM) files format using SAMTools44. Mark Duplicates in Picard tool (v1.102)45 was applied to remove repli-
cates reads and the two BAM files were used for subsequent analyses. Local realignment, InDels filtering and
calling were performed using a bioinformatics software Genome Analysis Tool Kit (GATK) version 3.1 (https://
gatk.broadinstitute.org/hc/en-us).
InDels flanking sequences and primers designing. Polymorphism analysis was performed following
the protocol described by Guo et al.46 with slight modification for establishing InDel polymorphisms between the
re-sequenced X1 and X2. To find out InDel polymorphisms between the re-sequenced X1 and X2, we explored
reference genome sequence of the Chinese fresh market type inbred line ‘9930’. The sequence reads for X1 and
X2 were aligned to the reference sequence individually through the Short Oligo-nucleotide Alignment Program
(SOAP) software47 with no gaps counts. The aligned reads dataset of X2 was compared to the InDel polymor-
phism dataset obtained upon mapping of X1 to the reference genome sequence. Only those InDels with identical
sequences arising from comparison with the Chinese fresh market type inbred line ‘9930’ were regarded as real
InDels for X1 and X2. Once the location of InDel polymorphisms for one re-sequenced parent and reference
genome sequence was established, those between the two re-sequenced parents became readily distinguishable
at corresponding positions where the second parent is identical to the reference sequence. To develop InDels
markers, 150-nucleotides sequences flanking both ends of an Insertion/Deletion site were extracted. A simple
Visual C++ script helped in fishing out these sequences from the reference genome sequence. The sequences
then served as templates for primers designing. Primer 5 (http://www.PromerBiosoft.com) was used to design
PCR primers with a varied range of properties (length of 18–28 bp, Tm of 57–63 °C, and PCR products of
80–300 bp).
DNA extraction and polymerase chain reaction. NuClear Plant Genomic DNA Kit (CWO531M)
(CW Biotech, Beijing, China) was used for total DNA extraction from the fresh leaves of 30-day old cucumber,
melon and watermelon plants (maintained under greenhouse condition) according to manufacturer’s recom-
mendation. The extracted DNA concentration was measured using Nanodrop spectrophotometer 2000 (Thermo
Scientific, USA) and adjusted to a final concentration of 50 ng/µl. A total volume of 25 µl PCR reaction mix
was prepared by composing 12.5 µl 2xTaq Master Mix plus loading buffer (CW Biotech, Beijing, China), 1 µl
forward, 1 µl reverse primer at a concentration of10 µM, 1 µl of DNA extract (50 ng/µl), and 9.5 µl of nuclease
free water. Amplification reaction conditions were as follows: initial denaturation at 94 °C for 2 min, 35 cycles of
denaturation at 94 °C for 30 s, annealing at 55 °C for 30 s, and extension at 72 °C for 30 s followed by 72 °C for
2 min. The PCR products were separated on a 2% agarose gel in 0.5× TAE buffer, stained with ethidium bromide
(EB) and visualized (UV) by Ultraviolet light at 300 nm using Gel imaging analyzer (WD-9413C, Bejing, China).
Cloning and sequencing. PCR products from X1 and X2 using a cross-species transferable marker
InDel114 and cross-parent transferable marker InDel79 were purified and ligated onto Psimple-19 Ecorv/BAP
Vector. Constructs (Psimple-19 EcorV/BAP—PCR fragment) were transformed into E. coli competent cells
(DH5α) followed by PCR verification with KOD FX enzyme (Toyobo Co., LTD, Japan). A 10 µl PCR reaction
contained 1 µl of transformed bacterial cell culture in solution, 5 µl of 2× PCR Buffer for KOD FX, 0.5 µl of for-
ward primer M13-F and reverse primers InDel114-R and InDel79-R (10 µM), 1 µl of dNTPs (2 mM), 0.2 µl of
KOD FX enzyme (1 units/µl) and 1.8 µl of double distilled water (ddH2O). PCR products were separated on aga-
rose gel, stained by EB and visualized by UV using Gel imaging analyzer. The positive clones were commercially
sequenced by Hangzhou Shangyasai Biotechnology Co. Ltd. The sequenced fragments nucleotide sequences
were aligned using the DNAMAN software (http://www.lynnon.com/).
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◂Figure 1. A display of cucumber lines fruits morphology and agarose gel resolvability of lnDel markers. Dense
spiny cucumber (A), female parent (B) and male parent (C) of Lvmei No.l hybrid variety, Lvmei No.l hybrid
variety (D), f ruit cucumber (E), White-green and black spiny cucumber (F), White green cucumber (G), White
Green sparsely spin y cucumber (H), Yellow Green sparsely spiny cucumber (I). Agarose gel electrophoresis
monograph for poly morphism analysis (J–Q); hybrid seeds purity detection (R–Y) and validation of lnDel
markers for 48 cucumber breeding lines (Z–AD); polymorphism analysis using lnDell69 (J), lnDel79 (K);
lnDel115 (L); lnDel117 (M), lnDel124 (N); lnDel170 (O); and In Del114 (P–Q); respectively; Hybrid seeds
purity testing of the elite cucumber hybrid va riety L vmei No.l using InDel79 (R); InDel170 (S), InDel114
(T–U), InDel124 (V), lnDel232 (W), InDel269 (X), and InDel48 (Y); respectively; Experimental validation of
48 cucumber breeding lines using In Del161 (Z); lnDel174 (AB), lnDel232 (AC), and lnDel269 (AD), X1 and
X2 are the parents of elite cucumber hybrid variety Lvmei No.l while C1/C2, C3/C4 and C5/C6 are 3 couples
of other three cucumber commercial hybrids while M1/M2, M3/M4 and M5/M6 constitute 3 couples for
three commercial melon hybrids; F1 represent individuals of Lvmei No.l; Allele 1, Allele2 and Allele3 are three
different allele generated from the 48 lines using InDel269; l = Dl, 2 = D2, 3 = D3, 4 = D4, 5 = D5, 6 = D6, 7 = D7,
8 = D8, 9 = D9, 10 = D10, 11 = D11, 12 = D12, 13 = D13, 14 = D14, 15 = D15, 16 = D16, 17 = D17, 18 = D18, 19
= D19, 20 = D20, 21 = D21, 22 = D22, 23 = D23, 24 = B1, 25 = B2, 26 = B3, 27 = B4, 28 = B5, 29 = B6, 30 = B7,
31 = B8, 32 = B9, 33 = X1, 34 = X2, 35 = X3, 36 = X4, 37 = X5, 38 = X6, 39 = X7, 40 = X8, 41 = X9, 42 = X10, 43 = X11,
44 = X12, 45 = X13, 46 = X14, 47 = X15, 48 = X16; M represents DL 2000 bp DNA Marker. The uncropped full-
length raw gel pictures are included in Supplementary Figure S1.
Samples Clean reads Map ratio (%) Cover ratio (%) Q20 (%) Depth
X1 187,403,732 97.36 97.30 97.05 15
X2 153,584,502 97.36 97.74 96.65 15
Average 170,494,117 97.36 97.52 96.85 15
Table 1. Detail information of cucumber hybrid variety Lvmei No.1 parents, X1 and X2.
X2 versus 9930 X1 versus X2
Chr. types Chr. PD (Mb) InDels number Frequency (InDels/Mb) InDels number Frequency (InDels/Mb)
Chr1 32.93 29,124 884.4 1734 52.7
Chr2 24.84 28,584 1150.7 1707 68.7
Chr3 40.88 45,372 1109.9 2289 56.0
Chr4 26.83 27,208 1014.1 1745 65.0
Chr5 31.91 22,479 704.5 1111 34.8
Chr6 31.13 28,438 913.5 1190 38.2
Chr7 22.47 16,959 754.7 694 30.9
Total 210.99 198,169 939.2 10,470 49.6
Table 2. Initially traced polymorphicInDel on X1 and X2 individual chromosomes with X2. Chr.:
Chromosome; Chr. PD: chromosome physical distance; Mb: megabase-pairs.
Genomic location of InDels. To predict the locus of the 68 InDel markers on the genome, the primer
sequences were used as query for a blast search in Gramene database (http://ensembl.gramene.org/Multi/Tools
/Blast?db=core) as compared to the reference sequence. The sequenced PCR products obtained using InDel114
and InDel79 primers were used to predict genomic location of these markers. NCBI (National Center for Biotech-
nology Database) database (https://www.ncbi.nlm.nih.gov/) and UNIPROT (https://www.uniprot.org/uniprot/
Q56X52) web based tools were successively used to obtain genes description and function of their derived loci.
Phylogenetic analysis. The amplified PCR products from the 48 breeding lines using 39 Cross-Parents
Transferable (CPT) polymorphic markers that cover 6 cucumber chromosomes were separated on agarose gel.
The obtained amplicons were scored according to the type of software deployed for the phylogenetic analysis.
Power Marker (PM) version 3.2548, is capable of exploiting quantitative data linked allele size (i.e., molecular
weight of allele) and was thus exploited for the aforementioned purpose. It was used to obtain the number of
alleles per locus, major allele frequency, gene diversity, values for polymorphism information content (PIC)
and to calculate Nei’s distance between breeding lines49. Phylogenetic tree was constructed with reference tothe
Nei’s minimum genetic distance based on UPGMA (unweighted pair group method using arithmetic average)
method and tree visualized with the help of MEGA 5.0 software (http://megasoftware.net/). NTSYS 2.150 and
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Type Length (bp) Deletion Insertion Total Percentage (%)
Small 1–10 2834 2849 5683 11.1
11–20 1412 1346 2758
Medium 35.0
21–30 500 440 940
Large > 30 598 573 1171 53.9
Total 5344 5208 10,552
Probability difference (InDel) 0.97
Table 3. Ranking of genome-wide InDels based on the length of nucleotide sequence.
Cross-
species
Strongly polymorphic (CPT) InDel
Indels markers markers
Species Hybrid varieties (breeding parents) 79 115 117 124 169 114 170
LvmeiNo.1 (X1&X2) √ √ √ √ √ √ √
C96/C1396 (C1&C2) √ √ √ √ √ √ √
Cucumber C87/C360 (C3&C4) √ √ √ √ √ √
C38/D18 (C5&C6) √ √ √ √ √ √ √
D52/C335 (C7&C8) √ √
M13065-1/39-1-1–1-1 (M1&M2) √
Melon M13065-1/17065-2-1(M3&M4) √
M170892/7305 (M5&M6) √
PK2-15/Q204 (W1&W2) √
Watermelon
PK2-18/74-1-3 (W3&W4)
Table 4. Polymorphism information of cross-parents and cross-species transferable InDel markers.
Darwin (i.e. Dissimilarity Analysis and Representation for Windows) version6 (http://Darwin.Cirad.fr), were
used for qualitative data analysis. The absent or present of allele was represented by 0 and 1, respectively.
Results
Identification and classification of genome‑wide Insertion/Deletion event. The clean reads
quantity generated was 187,403,732 for X1 and 153,584,502 for X2 recording with an average of 170,494,117.
Using the Burrows–Wheeler Alignment (BWA), 182,456,273 and 149,529,871 (average 165,993,072) reads from
X1 and X2, respectively were both mapped at a depth of 15 to the reference genome sequence of Chinese fresh
market type inbred line ‘9930’. The overall genome coverage was 97.30% for X1 and 97.74% for X2 hitting an
average of 95.8% (Table 1). Genome-wide insertion/deletion polymorphism generated 198,169 InDels between
X2 and 9930 measuring an InDels density of 939.2 InDels/Mb. The distribution of these InDels was among
the 7 (seven) chromosomes with variation in number recorded as follows: 16959 on chromosome07, 45372 on
chromosome03, 704.5 on chromosome05 and 1150.7 on chromosome02. Comparison of aligned reads between
X1 and X2 produced an average of 10,470 InDels and a density 49.6 InDels/Mb. These InDels span across the
seven cucumber chromosomes with chromosome07 recording the least (694) and chromosome03 the highest
(2289). There was equally a variation in the density that ranged from 30.9 InDels/Mb on chromosome7 to 68.7
InDels/Mb on chromosome02 (Table 2). In regards to the length of the nucleotide sequence, 3 types of Insertion/
Deletions were noticed and categorized as small, medium and large InDels. The differences in the number of
insertions and deletions for each type of InDel are minimal. The large, medium and small InDels accounted for
11.1%, 35% and 53.9% of the total genome-wide InDels, respectively (Table 3).
Agarose‑resolvable InDel markers for X1 and X2. The 10,470 InDels distributed over the seven-
cucumber chromosome were chosen for the development of PCR-based markers. The target fragment length
of 300 nucleotides for X1 and X2, known to harbor the corresponding Insertion/Deletion sites, were utilized as
templates for primers designing (Suppl. Table S2). With respect to the electrophoresis method applied, the poly-
acrylamide gel electrophoresis InDels PCR-based markers were consider to be those that falls under small and
medium InDels type and those belonging to large InDels type (with insertion/deletion size greater than 30 bp)
were categorized as agarose gel PCR-based markers. A total of 1171 PCR-based markers were identified with a
variation in the PCR products size ranging from 80 to 300 bp (Table 3). Out of 1171, the arbitrarily selected 385
candidate markers with an average density of 1.8 InDels/Mb were subjected to experimental validation (Supple-
mental Table 3). The InDels markers with an average density of 1.0 InDels/Mb that produced a single amplicons
with clear polymorphism between X1 and X2 accounted for 54.81% (211) of the 385 selected candidates. These
211 PCR-based InDels markers were recognized and considered as agarose-resolvable InDels markers (Suppl.
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Table S4). On the other hand, 174 representing 45.19% showed unclear or monomorphic bands under our PCR
conditions.
Identified cross‑parents and cross‑species transferable InDels markers. Five (5) pairs of cucum-
ber breeding parents were implicated in polymorphism analysis for validation of the considered agarose-
resolvable InDels markers. Sixty eight (68) InDel markers with an average density of 0.3 InDels/Mb revealed
polymorphism between more than 2 pairs of cucumber breeding parents (Suppl. Table S5) and were designated
as cross-parents transferable (CPT) Indels markers. Markers with remarkable polymorphic patterns between
more than 4 matches of breeding parents included InDel79, InDel115, InDel117, InDel124, InDel169, InDel114
and InDel170 (Fig. 1J–Q, Suppl. Figure S1, and Table 4). The cross-species transferability evaluation with these
markers was extended to three pairs of breeding parents from melon and two pairs from watermelon for poly-
morphism test. Interestingly, InDel114 and InDel177 expressed polymorphism between the breeding parents
derived from melon (Fig. 1J–Q) and from watermelon (Data not shown). To be brief, the number of agarose-
resolvable InDel markers recorded mark ranges from zero on chromosome07 to 59 on chromosome02 (Suppl.
Table 5). However, that of the cross-parents transferable markers varied from 0 to 44 on chromosome07 and
02, respectively while that of cross-species transferable InDel markers (with restricted variation) extended from
zero on chromosome02, 04, 05, 06, and 07 to two on chromosome03. Though the highest number of the InDels
between X1 and X2 was recorded for chromosome03, chromosome02 was predominant for agarose-resolvable
and CPT InDel markers (Suppl. Table 5).
Hybrids purity evaluation using InDel markers. In order to answer the question of how performing
these markers were on evaluating hybrid seed purity, seven of the InDel markers were selected for this purpose.
These markers included InDel114, InDel79, InDel170, InDel124, InDel232, InDel269 and InDel48 for genotyp-
ing of the hybrid seedlings of Lvmei No.1 variety and its corresponding parents X1 and X2. Herein, InDel114
which was shown to be transferable between cucumber and melon was used to test seeds purity for correspond-
ing melon hybrid variety. The outcome proved that these markers were capable to perform hybrid seeds purity
evaluation (Fig. 1R–Y, Suppl. Figure S1). The sequenced DNA fragment for accuracy confirmation of InDel114
yielded an amplicon of 191 nucleotides fragment length in cucumber male parent and 218 bp for female parent.
Further, these two DNA fragments (191 bp and 218 bp) were simultaneously amplified from the F1 individuals
(Fig. 1P, Suppl. Figure S2). Similarly, in melon, InDel114 generated 217 bp fragment length from male parent
and 253 bp from female parent as well as from the F1 individuals (Fig. 1Q, Suppl. Figure S2). On the other hand,
InDel79 amplified 204 bp fragment length from male parent and 151 bp from female parent accompanied with
the detection of both DNA fragment in F1 individuals as resolved by agarose gel electrophoresis (Fig. 1R, Suppl.
Figure S2).
Validation and application of InDel markers. To determine the PCR amplification versatility of these
CPT InDel markers, 68 primer pairs were used to amply the InDels from 48 cucumber breeding lines. These set
of primers were categorized based on the PCR amplicons from agarose gel electrophoresis. Of these primers,
both 29 pairs were not efficient by amplifying partial or not at all the targeted sequence from the 48 breeding
lines and such primers were thus excluded from this work. Thirty-nine (39) of these primer pairs generated at
least two alleles among the 48 breeding lines as presented in Fig. 1Z, AB, and AC for Indel161, Indel174 and
Indel232 respectively, with an exception of Indel269 that generated three alleles per locus (Fig. 1AD, Suppl.
Figure S1). However, non-group specific PCR amplicon was recorded for 27 pair of markers whereas 12 showed
specific amplification tendency for group1 breeding lines. Among these 12 InDel markers, InDel227, InDel232,
InDel265, InDel161, InDel172, InDel217, InDel48, InDel62, and InDel277 amplified a single identical allele
from breeding lines in group1 while InDel markers InDel225, InDel265, InDel171 and InDel41 generated a sin-
gle identical allele from breeding lines in group3. InDel269 could separate breeding lines in group1 from those
in group2 and group3 except for some six breeding lines in group1 (Fig. 1AD).
Polymorphism based on InDel markers. The allele frequency value of the 39 InDel markers used for
phylogenetic analysis was between 0.50 for InDel269 and 0.88 for InDel265. Allele number of two (2) was
observed for 38 InDel markers and three (3) for the InDel269 marker with an average of 2.03. The registered
genetic diversity ranged from 0.22 for InDel48 to 0.60 for InDel269 with an average value of 0.40. Apart from
InDel161with a heterozygosity score of 0.21, 38 others recorded zero making an average of 0.01. The least PIC
value was 0.20 and highest 0.52 as recorded by InDel48 and InDel269, respectively marking an average of 0.32
(Suppl. Table 6). Majority of these markers (~ 72%) recorded a PIC value comprised between 0.30 and 0.52. The
average PIC value for the night InDel markers that showed more specificity to group1 individuals registered an
average PIC value of 0.26 but the average PIC value for four InDel markers with high affinity for breeding lines
in group3 was 0.31. None group-specific InDel markers were 26 in number with an average PIC value of 0.33.
We found any of these InDel markers being specific for breeding lines in group2.
Phylogenetic analysis of cucumber breeding lines. Phylogenetic analysis results categorized the 48
breeding lines into two clusters designated as cluster I and cluster II. Cluster I constitutes 17 breeding lines of
which 71% of them belong to groupe 2 with majority of the individuals being fruit cucumber breeding lines of
the female parent X1 for Lvmei No.1 hybrid variety (Fig. 2, Suppl. Figure S3). Cluster II comprises of 31 cucum-
ber breeding lines. This includes individuals of group1 and group3 and the male parent X2 of Lvmei No.1 hybrid
variety (Fig. 2, Suppl. Figure S3). In brief, the 39 InDel markers could differentiate fruit cucumber varieties from
the common cucumbers with few exceptions. Power Marker software obtained results were further validated
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Figure 2. Radial display of phylogenetic trees constructed based on 39CPT InDel markers. Phylogenetic
tree constructed using Power Marker (PM) version 3.25 software (A) and Darwin version6 software (B). The
complete genome re-sequenced parents Xl and X2 of elite cucumber Lvmei No. 1 hybrid variety is highlighted
with triangular and round shape in black color. The red colored number in (B) indicates genetic similarity
score at root node of the tree. Numbers at each node in (B) are genetic similarity scores. In B: l = Dl , 2 = D2,
3 = D3, 4 = D4, 5 = D5, 6 = D6, 7 = D7, 8 = D8, 9 = D9, 10 = D10, 11 = D11, 12 = D12, 13 = D13, 14 = D14, 15 = D15,
16 = D16, 17 = D17, 18 = D18, 19 = D19, 20 = D20, 21 = D21, 22 = D22, 23 = D23, 24 = B1, 25 = B2, 26 = B3,
27 = B4, 28 = B5, 29 = B6, 30 = B7, 31 = B8, 32 = B9, 33 = X1, 34 = X2, 35 = X3, 36 = X4, 37 = X5, 38 = X6,
39 = X7, 40 = X8, 41 = X9, 42 = X10, 43 = X11, 44 = X12, 45 = X13, 46 = X14, 47 = X15, 48 = X16. The scale bars
represent the evolutionary time unit.
using Darwin and NTSYS softwares (Suppl. Figure S3). Intriguing, the pairwise genetic distance between parents
X1 and X2 was the highest as revealed by Nei’s genetic distance value of 0.96 (Suppl. Table S6).
Physical position and genomic location of the CPT InDel markers on cucumber chromo‑
somes. Physical map illustrated the corresponding positions of the 68 CPT InDel markers (Fig. 3). These
markers showed distribution across all the cucumber chromosomes, except for chromosome07, where a rela-
tively small number of agarose-resolvable markers was originally selected. In order to localize these CPT InDel
markers on the genome of cucumber, a blast search was performed from three different database platforms
including gramene database, NCBI and UNIPROT. Our search generated 16 InDel markers with position either
in the exon or in the intron of certain genes. The description and molecular function of these genes were recorded
which associated them to different potential functional activities. Among these 16 InDel markers, seven was
related to oxidoreductase activity, three to hydrolase activity (two for membrane trafficking and one for DNA
replication), one for RNA binding, one for protein biosynthesis and one for transferase activity (Suppl. Table S5).
Discussion
Myriad of activities related to domestication, natural and artificial selections have considerably restricted the
genetic variation of cultivated cucumber varieties. The identification of cucumber genotypes was traditionally
performed based on morphologically observed characteristics. Unfortunately, this approach is not definitely
efficient as plant morphology is easily influenced by environmental factors and in special cases of closely related
genotypes. In order to circumvent this short coming, different types of DNA markers have been developed for
better segregation of cultivars in cucumber breeding programs. Nowadays, SNPs, polyacrylamide-resolvable
InDels and SSR markers are the available and mostly used approaches in cucumber against RFLPs, AFLPs and
RAPD markers. Notwithstanding, genotyping using SNP requires a relatively complex platform coupled with the
fact that electrophoresis facilities of polyacrylamide-resolvable InDels and SSR markers are relatively expensive.
Strikingly, an alternative is the possibility of developing InDel markers for both polyacrylamide and agarose
gel electrophoresis with dependency on the size of insertion/deletion as mentioned by Liu et al.36,37. Recent
agarose-resolvable InDel markers approach was successfully developed for rice9. Though major breakthrough
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Figure 3. Physical map showing the distribution of the 68 CPT InDel markers on six chromosome of
cucumber.
has been made in the discovery of SSR markers as well as the most recent efforts deployed in the development
of InDel markers in cucumber20,42, no information is provided regarding their agarose gel resolvability during
electrophoresis. Unlike the polyacrylamide gel, breeders readily accept the agarose gel electrophoresis due to its
simplicity in term of usage and accessibility of required facilities.
In this study, agarose-resolvable InDel markers were developed based on whole-genome re-sequenced data
of cucumber breeding parents X1 and X2. With the concern of not discovering suitable InDel markers due to the
restricted genetic variation of cucumber, a relatively higher genome coverage ratio and sequencing depth were
applied. A total of 10,470 InDel markers were developed on seven cucumber chromosomes with exclusion of
those that are not anchored to any chromosome. More than a thousand InDels with insertion/deletion differences
equal to or more than 30 bp were chosen. In order to optimize time and scale up cost effectiveness, 385 markers
were selected in this study for experimental validation by agarose gel electrophoresis. Among these markers, 211
generated single PCR products (range 80 to 300 bp) with clear polymorphism resolvable on a 2% agarose gel.
In the year 2015, Liu and colleagues developed and reported InDel markers for rice of which the PCR products
varied between 150 and 300 bp resolvable on a 3.5% agarose gel over a long duration of electrophoresis36. It is
obvious that the large fragment insertions/deletions (InDel) of 30–55 bp differences can be exploited to amplify
DNA fragment of 300–350 bp which are easily separated on 1.5–2% agarose gel9. Sixty-eight among the one hun-
dred and eleven (211) InDel markers with clear polymorphism displayed polymorphism between the breeding
parents of more than 2 cucumber commercial varieties, thus depicting them as cross-parent transferable (CPT)
InDels markers in hybrid seeds purity test. There is the tendency that these markers can serve as an important
tool for rapid detection of seed purity and accession of genetic diversity in cucumber. A cross-species polymor-
phism was noticed with three of these InDel markers, but only InDel markers InDel114 exhibited transferability
between cucumber and melon as successful shown by our experiment.
In the past, molecular markers transferability has been reported between cucumber, melon and watermelon.
With emphasis on SSR markers and upon completion of draft genome assembly for these three crops19,20,23,51, a
large number of cross-species transferable SSR markers have been developed. This had equally open an avenue for
establishing a syntenic relationships among t hem19,22–24. The transferability aspect has been reported in previous
works stressing that there is a close relation between cucumber and melon than between cucumber and water-
melon. For example, an in silico PCR analysis using melon SSR markers resulted to the identification 4002 ampli-
cons between cucumber and melon while 1085 were found between watermelon and melon27. Specific genomic
regions have been defined using SSR products to reveal sequence homologies between cucumber and m elon52,53.
Moreover, SSR markers developed from melon have been used routinely in cucumber genetic mapping studies
and vice v ersa54,55. It is speculated that this tendency might be due to the fact that the specification of watermelon
has occurred earlier in Cucurbitaceae family56,57. Contrary, melon and cucumber diverged from a common
ancestor approximately ten million years ago2,58. The five cucumber chromosomes arose from fusions of ten
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melon ancestral chromosomes after divergence19 and chromosomes syntenic between melon and cucum-
ber are less complicated than that between melon and w atermelon27. Explicitly, the low discovering or failure of
obtaining polymorphic cross-species transferable InDel markers between cucumber and melon or watermelon
could be related to: few (3.68%) developed InDel markers were subjected to experimental validation; some InDel
markers have amplified cross-species genetic bands but with no polymorphism between the pairs of parents, thus
hampering their selection as we were concerned with polymorphic transferable markers; the number of pairs of
parents used for polymorphism analysis might be insufficient and the development of polymorphic cross-species
transferable markers was proceeded by initially evaluating their polymorphism in cucumber and then validating
the cross-transferability of this polymorphism in melon or watermelon. Our approach is reversed as compared to
that previously applied by Zhu and c olleagues27. Here, the unexploited 10,085 markers could constitute a potential
reservoir of agarose-resolvable InDels which require an experimental validation. However, the full exploitation
of the 10,470 InDel markers, together with an increase of pairs of breeding parents subjected to polymorphism
analysis in future experimental work might go a long way to increase the cross-species transferable InDel markers.
The cross-species transferable markers could be useful in map construction, comparative mapping, and genetic
diversity analysis in closely related species of cucurbit crops. The ability of these agarose-resolvable InDel markers
in PCR amplification versatility and evolutionary relation detection are demonstrated in a panel of 48 cucumber
selection lines. Here, these markers can effectively be used for research on genetic diversity and phylogenetic
relationships in cucumber. Impressively, they could clearly segregate the breeding lines in two principal clusters
with clusterI composed mainly of dense spiny cucumber (group1) and clusterII fruit cucumber varieties (group2).
The breeding lines of group3 were distributed between individuals in clusterI and II, indicating that they share
some similarities with genome fragments from dense spiny and fruit cucumber.
On the basis of genomic location of these markers, we speculated that the loci harboring these InDel markers
or their closely related genomic regions may be those participating in evolutionary divergence between parental
lineages of fruit and dense spiny cucumber from their common ancestor. In this study, the female and male par-
ent of Lvmei No.1 hybrid variety fall within the two clusters with the female parent grouped as fruit cucumber
in clusterII and male parent belonging to the dense spiny cucumber in cluster I. The female parent X1 here was
obtained after six generations of selfing of fruit cucumber hybrid variety HA-414 while the male parent X2 was a
single plant selected after crossing between fruit cucumber 22–403 and dense spiny cucumber Zhongnong No.26.
Therefore, the genetic background of X1 seems to be purely inherited from the fruit cucumber HA-414 while
that of X2 is mixed despite the fact that they are recognized as fruit cucumber lines. Evolutionary divergence
between lineages can be estimated using evolving characters, which are expressed via agronomical important
genes. Morphological similarity between these two parents could be explained by the fact that the genomic
regions carrying InDel markers used in phylogeny relationship construction may indirectly as well as not affecting
cucumber fruit phenotype. Numerous genes were reported and certain have been cloned from different tissues
of cucumber, including seedling, stem, leaf, flower and fruits as well as important disease resistance-related
genes59. Information on most cloned genes in cucumber can be found in NCBI database. In this regards, we
investigated and showed the location of those markers used in phylogenetic analysis. Most of them are located
in genes potentially associated to oxidoreductases and hydrolases activities. To the best of our knowledge these
newly developed polymorphic agarose-resolvable markers is the first of its type in cucumber and together with
the 66 CPT InDel markers are of great importance in cucumber research. This will go a long way in advancing
cucumber-breeding programs. They constitute a valuable genetic resource, which would benefit the cucumber
industry and breeding community.
Received: 25 June 2020; Accepted: 1 February 2021
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Acknowledgements
This work was supported by Suqian Science & Technology Program: 2017 Jiangsu Province Entrepreneurial
Innovation Talent Program and 2017 Suqian City Entrepreneurial Innovation Leading Talent Program funding.
Author contributions
Y.M.N.A. and L.T.S. conceived the idea; X.L., M.H.L. and X.Y. performed all the laboratory experiments, collected
the molecular data, Y.C.X., Q.Y.S., W.L., Z.J.D and W.T.Z. conducted the field experiments A.Y.M.N drafted the
manuscript, CGN gave critical revision of the manuscript. Md.A.A. prepared the manuscript according the Jour-
nal instructions to the authors. Y.M.N.A. designed the experiment, analyzed the data, and supervised the work.
Competing interests
The authors declare no competing interests.
Additional information
Supplementary Information The online version contains supplementary material available at https://doi.
org/10.1038/s41598-021-83313-x.
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